Open Access Highly Accessed Research article

Genomics of an extreme psychrophile, Psychromonas ingrahamii

Monica Riley1*, James T Staley2, Antoine Danchin3, Ting Zhang Wang3, Thomas S Brettin4, Loren J Hauser5, Miriam L Land5 and Linda S Thompson4

Author Affiliations

1 Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA

2 University of Washington, Seattle, WA 98195-7242, USA

3 Genetics of Bacterial Genomes, CNRS URA2171, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France

4 DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

5 Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA

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BMC Genomics 2008, 9:210  doi:10.1186/1471-2164-9-210

Published: 6 May 2008

Abstract

Background

The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles.

Results

Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins, at least one more than other bacteria, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3) there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4) one of the previously unseen clusters of proteins has a high proportion of "orphan" hypothetical proteins, raising the possibility these are cold-specific proteins.

Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2) P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3) P. ingrahamii has a large number (11) of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4) Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5) Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study.

Conclusion

The results of this genomic analysis provide a springboard for further investigations into mechanisms of psychrophily. Focus on the role of asparagine excess in proteins, targeted phenotypic characterizations and gene expression investigations are needed to ascertain if and how the organism regulates various proteins in response to growth at lower temperatures.